pairwiseEqual {alakazam}

Calculate pairwise equivalence between sequences

Description

pairwiseEqual determined pairwise equivalence between a pairs in a set of sequences, excluding ambiguous positions (Ns and gaps).

Usage

pairwiseEqual(seq)

Arguments

seq

character vector containing a DNA sequences.

Value

A logical matrix of equivalence between each entry in seq. Values are TRUE when sequences are equivalent and FALSE when they are not.

See Also

Uses seqEqual for testing equivalence between pairs. See pairwiseDist for generating a sequence distance matrix.

Examples

# Gaps and Ns will match any character
seq <- c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C", E="NTGGG")
d <- pairwiseEqual(seq)
rownames(d) <- colnames(d) <- seq
d